[gmx-users] query regarding atom type

durmaz at zib.de durmaz at zib.de
Sat Mar 27 16:26:50 CET 2010

hi there,

i'm doing simulation of protein-ligand systems since a few weeks and i've
been starting with a nice tutorial for acpypi (python script)


in order to create topology-files for several (42) ligands in an automized
way. works very fine so far.

changes, that i've applied to the tutorial: i don't add water at the
pdb2gmx step, but only later at the genbox step. in addition, i add the
include line for the water topology "manually" (script). however, if you
use acpypi, you should remove the coordinates/topology (section [
moleculetype ], [ atoms ], [ bonds ], ...)  of the protein from the
protein.top (generated by pdb2gmx) and create a own protein.itp file
containing that information, which than needs to be included in the
protein.top file.

restriction on acpypi: number of ligand's atoms is limited to about 200
(not sure).



> Hello All
> I am trying to add ions to my protein, for that I have run this command,,
> [sakshi at localhost ~/sonali]$ grompp -f ions.mdp -c protein_solv.gro -p
> topol.top -o ions.tpr
> and every time I run it, following error is coming
> Fatal error:
> Atomtype OA not found
> I am using OPLSA force field and I have a ligand in my molecule in which
> this atom type is there.
> I have tried to change the atom type after seeing force field's .itp file
> and
> I have also included ligand .itp file in topology file.
> But nothing is working for me.
> Please help
> Thanks in advance
> --
> Sonali Dhindwal
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